Computer analysis of sequence data
著者
書誌事項
Computer analysis of sequence data
（Methods in molecular biology / John M. Walker, series editor, v. 24-25）
Humana Press, c1994
- pt. 1
- pt. 2
大学図書館所蔵 全17件
注記
Includes index
内容説明・目次
- 巻冊次
-
pt. 1 ISBN 9780896032460
内容説明
DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gen- ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods ess- tial to analysis, and a familiarity with computers and sequence ana- sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Analysis of Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or p- tein) sequences. Each chapter is written such that a competent sci- tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed pr- tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes enco- tered by users of the sequence analysis software. Software packages for both the mainframe and personal computers are described.
目次
GCG: Fragment Assembly Programs. GCG: Drawing Linear Restriction Maps. GCG: Drawing Circular Restriction Maps. GCG: Displaying Restriction Sites and Possible Translations in a DNA Sequence. GCG: Assembly of Sequences into New Sequence Constructs. GCG: Comparison of Sequences. GCG: Production of Multiple-Sequence Alignment. GCG: Database Searching. GCG: Pattern Recognition. GCG: Translation of DNA Sequence. GCG: Analysis of Protein Sequences. GCG: The Analysis of RNA Secondary Structure. GCG: Preparing Sequence Data for Publication. MicroGenie: Introduction and Restriction Enzyme Analysis. MicroGenie: Shotgun DNA Sequencing. MicroGenie: Translation. MicroGenie: Protein Analysis. MicroGenie: Homology Searches. PC/GENE: Sequence Entry and Assembly. PC/GENE: Restriction Enzyme Analysis. PC/GENE: Translation and Searches for Protein Coding Regions. PC/GENE: Sequence Comparisons and Homologies. PC/GENE: Database Searches. PC/GENE: Searches for Functional Sites in Nucleic Acids and Proteins. Using the FASTA Program to Search Protein and DNA Sequence Databases. Converting Between Sequence Formats. Obtaining Software via INTERNET. Submission of Nucleotide Sequence Data to EMBL/GenBank/DDBJ. Index.
- 巻冊次
-
pt. 2 ISBN 9780896032767
内容説明
DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gener ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods essen tial to analysis, and a familiarity with computers and sequence analy sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Computer Analysis of Sequence Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or pro tein) sequences. Each chapter is written such that a competent scien tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed prac tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes encoun tered by users of the sequence analysis software.
目次
Staden: Introduction. Staden: Sequence Input, Editing, and Sequence Library Use. Staden: Managing Sequence Projects. Staden: Statistical and Structural Analysis of Nucleotide Sequences. Staden: Searching for Restriction Sites. Staden: Translating and Listing Nucleic Acid Sequences. Staden: Searching for Motifs in Nucleic Acid Sequences. Staden: Using Patterns to Analyze Nucleic Acid Sequences. Staden: Analyzing Sequences to Find Genes. Staden: Statistical and Structural Analysis of Protein Sequences. Staden: Searching for Motifs in Protein Sequences. Staden: Using Patterns to Analyze Protein Sequences. Staden: Comparing Sequences. Staden Plus. DNA Strider: A Macintosh Program for Handling Protein and Nucleic Acid Sequences. MacVector: An Integrated Sequence Analysis Program for the Macintosh. MacVector: Aligning Sequences. MacVector: Sequence Comparisons Using a Matrix Method. MacVector: Restriction Enzyme Analysis. MacVector: Protein Analysis. Profile Analysis. Prediction of RNA Secondary Structure by Energy Minimization. Classification and Function Prediction of Proteins Using Diagnostic Amino Acid Patterns. CLUSTAL V: Multiple Alignment of DNA and Protein Sequences. Progressive Multiple Alignment of Protein Sequences and the Construction of Phylogenetic Trees. The AMPS Package for Multiple Protein Sequence Alignment. TreeAlign. Using the FASTA Program to Search Protein and DNA Sequence Databases. Converting Between Sequence Formats. Obtaining Software via INTERNET. Submission of Nucleotide Sequence Data to EMBL/GenBank/DDBJ. Index.
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